Non-equilibrium Markov state modeling of periodically driven biomolecules

Molecular dynamics simulations allow us to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained multiscale models. While systematic approaches to construc...

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Veröffentlicht in:The Journal of chemical physics 2019-02, Vol.150 (5), p.054103-054103
Hauptverfasser: Knoch, Fabian, Speck, Thomas
Format: Artikel
Sprache:eng
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Zusammenfassung:Molecular dynamics simulations allow us to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained multiscale models. While systematic approaches to construct such models have become available, these typically rely on microscopic dynamics that obey detailed balance. In vivo, however, biomolecules are constantly driven away from equilibrium in order to perform specific functions and thus break detailed balance. Here we introduce a method to construct Markov state models for systems that are driven through periodically changing one (or several) external parameter. We illustrate the method for alanine dipeptide, a widely used benchmark molecule for computational methods, exposed to a time-dependent electric field.
ISSN:0021-9606
1089-7690
DOI:10.1063/1.5055818